|
0
|
1 gfop
|
|
|
2 Function
|
|
|
3
|
|
|
4 Calculate the frequency of optimal codons (Fop)
|
|
|
5
|
|
|
6 Description
|
|
|
7
|
|
|
8 gfop calculates the frequency of optimal codons (Fop).Fop is an index to
|
|
|
9 show the optimization level of synonymous codon usage choice. It is
|
|
|
10 basically a ratio of optimal codons against all codons used. The value
|
|
|
11 of Fop ranges from 0 (no optimal codons are used) and 1 (only optimal
|
|
|
12 codons are used).
|
|
|
13
|
|
|
14 G-language SOAP service is provided by the
|
|
|
15 Institute for Advanced Biosciences, Keio University.
|
|
|
16 The original web service is located at the following URL:
|
|
|
17
|
|
|
18 http://www.g-language.org/wiki/soap
|
|
|
19
|
|
|
20 WSDL(RPC/Encoded) file is located at:
|
|
|
21
|
|
|
22 http://soap.g-language.org/g-language.wsdl
|
|
|
23
|
|
|
24 Documentation on G-language Genome Analysis Environment methods are
|
|
|
25 provided at the Document Center
|
|
|
26
|
|
|
27 http://ws.g-language.org/gdoc/
|
|
|
28
|
|
|
29 Usage
|
|
|
30
|
|
|
31 Here is a sample session with gfop
|
|
|
32
|
|
|
33 % gfop refseqn:NC_000913
|
|
|
34 Calculate the frequency of optimal codons (Fop)
|
|
|
35 Codon usage output file [nc_000913.gfop]:
|
|
|
36
|
|
|
37 Go to the input files for this example
|
|
|
38 Go to the output files for this example
|
|
|
39
|
|
|
40 Command line arguments
|
|
|
41
|
|
|
42 Standard (Mandatory) qualifiers:
|
|
|
43 [-sequence] seqall Nucleotide sequence(s) filename and optional
|
|
|
44 format, or reference (input USA)
|
|
|
45 [-outfile] outfile [*.gfop] Codon usage output file
|
|
|
46
|
|
|
47 Additional (Optional) qualifiers: (none)
|
|
|
48 Advanced (Unprompted) qualifiers:
|
|
|
49 -translate boolean [N] Include when translates using standard
|
|
|
50 codon table
|
|
|
51 -[no]accid boolean [Y] Include to use sequence accession ID as
|
|
|
52 query
|
|
|
53
|
|
|
54 Associated qualifiers:
|
|
|
55
|
|
|
56 "-sequence" associated qualifiers
|
|
|
57 -sbegin1 integer Start of each sequence to be used
|
|
|
58 -send1 integer End of each sequence to be used
|
|
|
59 -sreverse1 boolean Reverse (if DNA)
|
|
|
60 -sask1 boolean Ask for begin/end/reverse
|
|
|
61 -snucleotide1 boolean Sequence is nucleotide
|
|
|
62 -sprotein1 boolean Sequence is protein
|
|
|
63 -slower1 boolean Make lower case
|
|
|
64 -supper1 boolean Make upper case
|
|
|
65 -scircular1 boolean Sequence is circular
|
|
|
66 -sformat1 string Input sequence format
|
|
|
67 -iquery1 string Input query fields or ID list
|
|
|
68 -ioffset1 integer Input start position offset
|
|
|
69 -sdbname1 string Database name
|
|
|
70 -sid1 string Entryname
|
|
|
71 -ufo1 string UFO features
|
|
|
72 -fformat1 string Features format
|
|
|
73 -fopenfile1 string Features file name
|
|
|
74
|
|
|
75 "-outfile" associated qualifiers
|
|
|
76 -odirectory2 string Output directory
|
|
|
77
|
|
|
78 General qualifiers:
|
|
|
79 -auto boolean Turn off prompts
|
|
|
80 -stdout boolean Write first file to standard output
|
|
|
81 -filter boolean Read first file from standard input, write
|
|
|
82 first file to standard output
|
|
|
83 -options boolean Prompt for standard and additional values
|
|
|
84 -debug boolean Write debug output to program.dbg
|
|
|
85 -verbose boolean Report some/full command line options
|
|
|
86 -help boolean Report command line options and exit. More
|
|
|
87 information on associated and general
|
|
|
88 qualifiers can be found with -help -verbose
|
|
|
89 -warning boolean Report warnings
|
|
|
90 -error boolean Report errors
|
|
|
91 -fatal boolean Report fatal errors
|
|
|
92 -die boolean Report dying program messages
|
|
|
93 -version boolean Report version number and exit
|
|
|
94
|
|
|
95 Input file format
|
|
|
96
|
|
|
97 The database definitions for following commands are available at
|
|
|
98 http://soap.g-language.org/kbws/embossrc
|
|
|
99
|
|
|
100 gfop reads one or more nucleotide sequences.
|
|
|
101
|
|
|
102 Output file format
|
|
|
103
|
|
|
104 The output from gfop is to a plain text file.
|
|
|
105
|
|
|
106 File: nc_000913.gfop
|
|
|
107
|
|
|
108 Sequence: NC_000913
|
|
|
109 Laa,Lc,fop,gene
|
|
|
110 20,5,0.4000,thrL
|
|
|
111 819,133,0.4361,thrA
|
|
|
112 309,46,0.4783,thrB
|
|
|
113 427,69,0.5217,thrC
|
|
|
114 97,7,0.2857,yaaX
|
|
|
115 257,56,0.4643,yaaA
|
|
|
116 475,96,0.3958,yaaJ
|
|
|
117 316,56,0.6964,talB
|
|
|
118
|
|
|
119 [Part of this file has been deleted for brevity]
|
|
|
120
|
|
|
121 169,27,0.2593,yjjX
|
|
|
122 214,23,0.5652,ytjC
|
|
|
123 288,49,0.4082,rob
|
|
|
124 156,23,0.3478,creA
|
|
|
125 228,26,0.3462,creB
|
|
|
126 473,69,0.3478,creC
|
|
|
127 449,70,0.3286,creD
|
|
|
128 237,46,0.6957,arcA
|
|
|
129 45,10,0.7000,yjjY
|
|
|
130 227,24,0.2500,yjtD
|
|
|
131
|
|
|
132
|
|
|
133 Data files
|
|
|
134
|
|
|
135 None.
|
|
|
136
|
|
|
137 Notes
|
|
|
138
|
|
|
139 None.
|
|
|
140
|
|
|
141 References
|
|
|
142
|
|
|
143 Ikemura, T. (1981) Correlation between the abundance of Escherichia coli
|
|
|
144 transfer RNAs and the occurrence of the respective codons in its protein
|
|
|
145 genes: a proposal for a synonymous codon choice that is optimal for the
|
|
|
146 E. coli translational system, J.Mol.Biol, 151:389-409.
|
|
|
147
|
|
|
148 Ikemura (1985) Codon usage and tRNA content in unicellular and multicellular
|
|
|
149 organisms, Mol.Biol.Evol, 2(1):13-34.
|
|
|
150
|
|
|
151 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
|
|
|
152 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
|
|
|
153 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
|
|
|
154
|
|
|
155 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
|
|
|
156 large-scale analysis of high-throughput omics data, J. Pest Sci.,
|
|
|
157 31, 7.
|
|
|
158
|
|
|
159 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
|
|
|
160 Analysis Environment with REST and SOAP Web Service Interfaces,
|
|
|
161 Nucleic Acids Res., 38, W700-W705.
|
|
|
162
|
|
|
163 Warnings
|
|
|
164
|
|
|
165 None.
|
|
|
166
|
|
|
167 Diagnostic Error Messages
|
|
|
168
|
|
|
169 None.
|
|
|
170
|
|
|
171 Exit status
|
|
|
172
|
|
|
173 It always exits with a status of 0.
|
|
|
174
|
|
|
175 Known bugs
|
|
|
176
|
|
|
177 None.
|
|
|
178
|
|
|
179 See also
|
|
|
180
|
|
|
181 genc Calculate the effective number of codons (Nc)
|
|
|
182 gew Calculate a measure of synonymous codon usage evenness (Ew)
|
|
|
183 gscs Calculates the scaled chi-square
|
|
|
184 gwvalue Calculate the 'relative adaptiveness of each codon' (W)
|
|
|
185
|
|
|
186 Author(s)
|
|
|
187
|
|
|
188 Hidetoshi Itaya (celery@g-language.org)
|
|
|
189 Institute for Advanced Biosciences, Keio University
|
|
|
190 252-0882 Japan
|
|
|
191
|
|
|
192 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
|
|
|
193 Institute for Advanced Biosciences, Keio University
|
|
|
194 252-0882 Japan
|
|
|
195
|
|
|
196 History
|
|
|
197
|
|
|
198 2012 - Written by Hidetoshi Itaya
|
|
|
199 2013 - Fixed by Hidetoshi Itaya
|
|
|
200
|
|
|
201 Target users
|
|
|
202
|
|
|
203 This program is intended to be used by everyone and everything, from
|
|
|
204 naive users to embedded scripts.
|
|
|
205
|
|
|
206 Comments
|
|
|
207
|
|
|
208 None.
|
|
|
209
|
